Struct MinimizerBuilder

pub struct MinimizerBuilder<T: PrimInt = u64, A: MinimizerAlgorithm = Minimizer, S: BuildHasher = DefaultHashBuilder, const CANONICAL: bool = false> { /* private fields */ }

A builder for iterators over minimizers.

Examples

use minimizer_iter::MinimizerBuilder;

// Build an iterator over minimizers
// of size 3 with a window of size 4
// for the sequence "TGATTGCACAATC"
let min_iter = MinimizerBuilder::<u64>::new()
    .minimizer_size(3)
    .width(4)
    .iter(b"TGATTGCACAATC");

for (minimizer, position) in min_iter {
    // ...
}

Implementations

impl<T: PrimInt + Hash> MinimizerBuilder<T>

pub fn new() -> Self

Sets up the MinimizerBuilder with default values:

• minimizer_size = 21
• width = 11 (31 - 21 + 1)
• hasher = DefaultHashBuilder
• encoding: A = 00, C = 01, G = 10, T = 11

impl<T: PrimInt + Hash, S: BuildHasher> MinimizerBuilder<T, Minimizer, S, false>

pub fn iter(self, seq: &[u8]) -> MinimizerIterator<'_, T, S>

Builds an iterator over the minimizers and their positions in the given sequence.

pub fn iter_pos(self, seq: &[u8]) -> MinimizerPosIterator<'_, T, S>

Builds an iterator over the positions of the minimizers in the given sequence.

impl<T: PrimInt + Hash, S: BuildHasher> MinimizerBuilder<T, Minimizer, S, true>

pub fn iter(self, seq: &[u8]) -> CanonicalMinimizerIterator<'_, T, S>

Builds an iterator over the canonical minimizers and their positions in the given sequence with a boolean indicating a reverse complement. It requires an odd width to break ties between multiple minimizers.

pub fn iter_pos(self, seq: &[u8]) -> CanonicalMinimizerPosIterator<'_, T, S>

Builds an iterator over the positions of the canonical minimizers in the given sequence with a boolean indicating a reverse complement. It requires an odd width to break ties between multiple minimizers.

impl<T: PrimInt + Hash> MinimizerBuilder<T, ModMinimizer>

pub fn new_mod() -> Self

Sets up the MinimizerBuilder for mod-minimizers with default values:

• minimizer_size = 21
• width = 11 (31 - 21 + 1)
• hasher = DefaultHashBuilder
• encoding: A = 00, C = 01, G = 10, T = 11

impl<T: PrimInt + Hash, S: BuildHasher> MinimizerBuilder<T, ModMinimizer, S, false>

pub fn iter(self, seq: &[u8]) -> ModSamplingIterator<'_, T, S>

Builds an iterator over the mod-minimizers and their positions in the given sequence.

pub fn iter_pos(self, seq: &[u8]) -> ModSamplingPosIterator<'_, T, S>

Builds an iterator over the positions of the mod-minimizers in the given sequence.

impl<T: PrimInt + Hash, S: BuildHasher> MinimizerBuilder<T, ModMinimizer, S, true>

pub fn iter(self, seq: &[u8]) -> CanonicalModSamplingIterator<'_, T, S>

Builds an iterator over the canonical mod-minimizers and their positions in the given sequence with a boolean indicating a reverse complement. It requires an odd width to break ties between multiple minimizers.

pub fn iter_pos(self, seq: &[u8]) -> CanonicalModSamplingPosIterator<'_, T, S>

Builds an iterator over the positions of the canonical mod-minimizers in the given sequence with a boolean indicating a reverse complement. It requires an odd width to break ties between multiple minimizers.

impl<T: PrimInt + Hash, A: MinimizerAlgorithm> MinimizerBuilder<T, A, DefaultHashBuilder>

pub fn seed(self, seed: u64) -> Self

Sets the seed of the default hasher.

impl<T: PrimInt + Hash, A: MinimizerAlgorithm, S: BuildHasher, const CANONICAL: bool> MinimizerBuilder<T, A, S, CANONICAL>

pub fn minimizer_size(self, minimizer_size: usize) -> Self

Sets the size of the minimizers.

pub const fn width(self, width: u16) -> Self

Sets the width of the window.

pub fn hasher<H: BuildHasher>( self, hasher: H, ) -> MinimizerBuilder<T, A, H, CANONICAL>

Sets the hasher used to compute minimizers.

pub fn encoding(self, a: u8, c: u8, g: u8, t: u8) -> Self

Sets the binary encoding of the bases.

pub fn canonical(self) -> MinimizerBuilder<T, A, S, true>

Compute canonical minimizers.

pub fn non_canonical(self) -> MinimizerBuilder<T, A, S, false>

Compute non-canonical minimizers.

Trait Implementations

impl<T: Clone + PrimInt, A: Clone + MinimizerAlgorithm, S: Clone + BuildHasher, const CANONICAL: bool> Clone for MinimizerBuilder<T, A, S, CANONICAL>

fn clone(&self) -> MinimizerBuilder<T, A, S, CANONICAL>

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl<T: Debug + PrimInt, A: Debug + MinimizerAlgorithm, S: Debug + BuildHasher, const CANONICAL: bool> Debug for MinimizerBuilder<T, A, S, CANONICAL>

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl<T: PrimInt + Hash> Default for MinimizerBuilder<T>

fn default() -> Self

Returns the “default value” for a type.

impl<T: PartialEq + PrimInt, A: PartialEq + MinimizerAlgorithm, S: PartialEq + BuildHasher, const CANONICAL: bool> PartialEq for MinimizerBuilder<T, A, S, CANONICAL>

fn eq(&self, other: &MinimizerBuilder<T, A, S, CANONICAL>) -> bool

Tests for self and other values to be equal, and is used by ==.

fn ne(&self, other: &Rhs) -> bool

Tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl<T: Eq + PrimInt, A: Eq + MinimizerAlgorithm, S: Eq + BuildHasher, const CANONICAL: bool> Eq for MinimizerBuilder<T, A, S, CANONICAL>

impl<T: PrimInt, A: MinimizerAlgorithm, S: BuildHasher, const CANONICAL: bool> StructuralPartialEq for MinimizerBuilder<T, A, S, CANONICAL>